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110 lines
4.5 KiB
ReStructuredText
110 lines
4.5 KiB
ReStructuredText
Building the ``kaiju`` software on Ubuntu 20.04
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===============================================
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.. Introduction
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.. ------------
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.. This page provides instructions for building the ``kaiju`` software on an
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.. Intel-based Ubuntu 20.04 system. These instructions were developed for using a
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.. Ubuntu 20.04 virtual machine running under VirtualBox on a Mac, but the
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.. instructions should work for other Linux distributions, although minor changes
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.. may be needed, especially if your Linux distribution does no use the ``apt``
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.. package manager.
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.. Step 0: Prepare your system
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.. ---------------------------
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.. A few tools must be installed on your system before you begin building the
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.. ``kaiju`` software. These instructions assume you have permission to use
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.. ``sudo`` to install software.
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.. .. code-block:: shell
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.. sudo apt-get install build-essential
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.. sudo apt-get install cmake
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.. sudo apt-get install git
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.. sudo apt-get install git-lfs
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.. sudo apt-get install libgeos-dev
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.. sudo apt-get install pkg-config
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.. Install the Intel compiler suite
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.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. The ``kaiju`` software is developed using the Intel compiler suite, available
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.. `here <https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html#gs.29x43u>`_.
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.. The compiler suite is free, but comes in several optional parts. You will need
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.. to install the `Intel oneAPI Base Toolkit <https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit-download.html>`_
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.. and the `Intel oneAPI HPC Toolkit <https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit-download.html>`_.
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.. Once installed, this software should be available on your system under
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.. ``/opt/intel``.
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.. Once the Intel tools are installed, you will need to make them available
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.. during the build process. Set up the tools as follows:
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.. .. code-block:: shell
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.. source /opt/intel/oneapi/setvars.sh
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.. Step 1: Build prerequisite libraries
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.. ------------------------------------
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.. NASA CDF library
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.. ~~~~~~~~~~~~~~~~
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.. The `NASA CDF (Common Data Format) library <https://cdf.gsfc.nasa.gov/>`_ is
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.. used in parts of the ``kaiju`` post-processing software when fetching
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.. spacecraft data from `CDAWeb <https://cdaweb.gsfc.nasa.gov/>`_. Prior to
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.. building the ``kaiju`` software, the CDF library must be built and installed
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.. on your system, since it is not available via the ``apt`` package manager.
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.. Instructions for building and installing the CDF library on your system are
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.. available :doc:`here <ubuntu-20.04_build_cdf>`.
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.. HDF5 library
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.. ~~~~~~~~~~~~
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.. The `HDF5 <https://www.hdfgroup.org/solutions/hdf5/>`_ file format is used
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.. extensively for data storage in the ``kaiju`` software. The HDF5 software is
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.. available via ``apt``, but this version will not link with the ``kaiju``
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.. software when built with the Intel compiler suite. Prior to building the
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.. ``kaiju`` software, the HDF5 library must be built and installed on your
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.. system.
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.. Instructions for building and installing the HDF5 library on your system are
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.. available :doc:`here <ubuntu-20.04_build_hdf5>`.
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.. NOTE: If you successfully build the ``kaiju`` software using the
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.. ``apt``-installed version of HDF5 on Ubuntu 20.04, please let us know how you
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.. did it!
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.. Step 2: Create a python environment
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.. -----------------------------------
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.. Most of the ``kaiju`` software for pre-processing, post-processing, and
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.. analysis is written in `Python <https://www.python.org/>`_. Python is
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.. available in many forms (or 'distributions'), but we recommend use of the
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.. `Miniconda distribution <https://docs.conda.io/en/latest/miniconda.html>`_
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.. for simplicity and compactness.
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.. Instructions for installing python and building a python environment on your
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.. system are available :doc:`here <ubuntu-20.04_build_python>`.
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.. Step 3: Compile the ``kaiju`` software
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.. --------------------------------------
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.. The ``kaiju`` software can be built in serial or MPI versions. The serial
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.. version should be used when running the code on a single computer. The MPI
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.. version should be used when running on an HPC system (a supercomputer).
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.. Instructions for building the serial version of the ``kaiju`` software on
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.. Ubuntu 20.04 are available :doc:`here <ubuntu-20.04_build_kaiju>`. The MPI
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.. version of ``kaiju`` is not supported on Ubuntu 20.04 at this time.
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.. toctree::
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:maxdepth: 1
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ubuntu-20.04_build_cdf
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ubuntu-20.04_build_hdf5
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ubuntu-20.04_build_kaiju
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ubuntu-20.04_build_python |